This conference brought the microbial genomics community together to share their most up-to-the-minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross-section of the talks from the sessions on 'Genome analysis and comparative genomics', 'Computational genomics' and 'Functional genomi...

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such...

Whole-Genome Alignments and Polytopes for Comparative Genomics

was coined in 1920 (see Chapter 1), the general concept goes back at least as far as the 4th century BCE, when Aristotle implicated blood as the heredity substance. The blood of the mother, it was thought, supplied matter to the developing fetus whereas the semen (a purified form of blood) of the father conveyed form (Aristotle, 1953). Ironically, although the notions of “blood relations” and c...

Over the last couple of decades, numerous genetic and physical maps have been developed for a wide range of species. This has led to the field of comparative genomics which analyses characteristics of whole genomes, in contrast to the analysis of single genes in comparative genetics. Where markers on one map are known to be have homologues on another, we can get a feel for the relative distribu...

W. Ansorge V. De Lorenzo U. Landegren H. Schwab P.-A. Binz M. Dunn I. Lefkovits J. Smeitink S. Brunak J. Engels P. Legrain C. Thompson D. Cahill A. Goffeau M. Linial M. Uhlen P. Ceglowski A. Henriques A. Mespalu A. Valencia J. Celis D. Higgins C. Mundy G.-J. van Ommen M. Helmer Citterich J. Hoheisel M. Özgűc A. Varadi A. Danchin T. Joos W. Patsch E. Vuorio A. de Daruvar J. Kolarov H. Prydz R. Z...

E. R # Sp Data Growth over the Years . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211 Taxonomy Analysis, Most Sequenced Phyla and Genera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212 Basic Genome Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Thousands of Genome Sequences . . . . . . . . . . . . . ....

Motivation: Genomes contain the information for constructing organisms. In some sense, this information is put in by selection, and it is degraded by mutation and genetic drift. It is natural to pose some basic questions of principle. What is the maximum amount of information that can be maintained at mutation-selection equilibrium? Can organisms in principle become arbitrarily complex, or, for...

Comparative sequence analysis has become a widespread approach for identifying and characterizing functional elements encoded within genomic sequences. Marked by early successes (for review, see Hardison 2000), a tremendous amount of sequencing capacity has been, and continues to be, utilized for sequencing genomes of related species. Indeed, the choice of genomes selected for sequencing has le...

The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently,...